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- PDB-5z34: The structure of a chitin deacetylase from Bombyx mori provide th... -

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Basic information

Entry
Database: PDB / ID: 5z34
TitleThe structure of a chitin deacetylase from Bombyx mori provide the first insight into insect chitin deacetylation mechanism
ComponentsChitin deacetylase
KeywordsHYDROLASE / Chitin deacetylase / Bombyx mori / activity / chitin binding
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.399 Å
AuthorsLiu, L. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Funds for Distinguished Young Scholar31425021 China
Citation
Journal: To Be Published
Title: The structure of a chitin deacetylase from Bombyx mori provide the first insight into insect chitin deacetylation mechanism
Authors: Liu, L. / Zhou, Y. / Yang, Q.
#1: Journal: INSECT MOL.BIOL. / Year: 2017
Title: The physiological differentiation along the midgut of Bombyx mori-inspirations from the proteomics and gene expression patterns of the secreted proteins in the ectoperitrophic space
Authors: Liu, L. / Qu, M. / Yang, J. / Yang, Q.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8253
Polymers42,3351
Non-polymers4902
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-31 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.017, 115.017, 106.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chitin deacetylase /


Mass: 42334.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Komagataella pastoris GS115 (fungus) / References: chitin deacetylase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN IS NOT AVAILABLE IN UNIPROT AT THE TIME OF DATA PROCESSING. THE ...THE SEQUENCE OF THE PROTEIN IS NOT AVAILABLE IN UNIPROT AT THE TIME OF DATA PROCESSING. THE SEQUENCE IS BASED ON NCBI Reference Sequence XP_004923455.1. SIGNAL PEPTIDE ON N-TERMINAL (RESIDUES 1-18) WERE NOT EXPRESSED. AND HIS-TAG (HHHHHH) WAS ADDED C-TERMINAL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.02M Calcium chloride dihydrate, 0.1M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32284 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 37.59 Å2 / CC1/2: 0.834 / Net I/σ(I): 3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1815 / CC1/2: 0.907 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
HKL-3000data reduction
RefinementResolution: 2.399→46.964 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 1555 5.37 %
Rwork0.175 --
obs0.1759 28976 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→46.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 29 160 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013039
X-RAY DIFFRACTIONf_angle_d1.0974159
X-RAY DIFFRACTIONf_dihedral_angle_d17.7981112
X-RAY DIFFRACTIONf_chiral_restr0.069442
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3986-2.4760.24131300.22022163X-RAY DIFFRACTION79
2.476-2.56450.23121160.212260X-RAY DIFFRACTION82
2.5645-2.66720.22921520.20752303X-RAY DIFFRACTION85
2.6672-2.78860.22891390.21112344X-RAY DIFFRACTION85
2.7886-2.93560.2221480.19612455X-RAY DIFFRACTION90
2.9356-3.11950.20741660.19412509X-RAY DIFFRACTION92
3.1195-3.36030.21821180.18482643X-RAY DIFFRACTION94
3.3603-3.69830.16441340.17982682X-RAY DIFFRACTION96
3.6983-4.23310.15121420.15422737X-RAY DIFFRACTION97
4.2331-5.33210.17061610.14772675X-RAY DIFFRACTION96
5.3321-46.9730.19941490.16822650X-RAY DIFFRACTION90

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